A Small Protein

The goal of this tutorial is the simulation of a small protein and one of its mutants. The protein, called chignolin, is a designed protein of 10 amino acid residues that, when synthesized, shows a stable 3D structure in aqueous solution (see S. Honda, K. Yamasaki, Y. Sawada and H. Morii. 10 Residue Folded Peptide Designed by Segment Statistics. Structure 12, 1507–1518 (2004) [Link]).
The
size of the protein means that molecular dynamics simulations of
reasonable length can be carried out without using excessive computer
resources.

This tutorial is more advanced than some of the others in the
pDynamo distribution as a detailed guide of how to perform each of the
tasks is not given. Instead readers are encouraged to find their own
solutions.

The steps in the tutorial are given below whereas programs
implementing possible solutions to each of the tasks may be found in the
tutorials/aSmallProtein subdirectory of the pDynamo distribution.